Magnetic nanoparticle-mediated isolation of functional bacteria in a complex microbial community

ISME Journal

Volumn 9, Issue 3, 2015, Pages 603-614

  Zhang, Dayi ^a   Berry, James P ^a   Zhu, Di ^a   Wang, Yun ^b   Chen, Yin ^c   Jiang, Bo ^d   Huang, Shi ^b   Langford, Harry ^a   Li, Guanghe ^d   Davison, Paul A ^a   Xu, Jian ^b   Aries, Eric ^e   Huang, Wei E ^a  

^a UNIVERSITY OF SHEFFIELD   (United Kingdom)

^b INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^c UNIVERSITY OF WARWICK   (United Kingdom)

^d TSINGHUA UNIVERSITY   (China)

^e SWINDEN TECHNOLOGY CENTRE   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

ECOPHYSIOLOGY; MICROBIAL COMMUNITY; MICROORGANISM; PHENOL; SLUDGE; WASTEWATER;

BACTERIA (MICROORGANISMS); BURKHOLDERIALES; CHRYSEOBACTERIUM; PSEUDOMONAS; RHODOCOCCUS SP.;

BACTERIAL DNA; MAGNETITE NANOPARTICLE; PHENOL; RNA 16S; SEWAGE; WASTE WATER;

BETAPROTEOBACTERIA; BIOREMEDIATION; CHEMISTRY; EVALUATION STUDY; GENETICS; ISOLATION AND PURIFICATION; MAGNETISM; METABOLISM; MICROBIOLOGY; PROCEDURES; SEWAGE; WASTE WATER;

BETAPROTEOBACTERIA; BIODEGRADATION, ENVIRONMENTAL; DNA, BACTERIAL; MAGNETICS; MAGNETITE NANOPARTICLES; PHENOL; RNA, RIBOSOMAL, 16S; SEWAGE; WASTE WATER;

EID: 84923332693     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2014.161     Document Type: Article

References (34)

1. Arp DJ, Sayavedra-Soto LA, Hommes NG. (2002). Molecular biology and biochemistry of ammonia oxidation by Nitrosomonas europaea. Arch Microbiol 178: 250-255.
2. Bauchop T, Elsden SR. (1960). The growth of microorganisms in relation to their energy supply. J Gen Microbiol 23: 457-469.
3. Bombach P, Chatzinotas A, Neu TR, Kaestner M, Lueders T, Vogt C. (2010). Enrichment and characterization of a sulfate-reducing toluene-degrading microbial consortium by combining in situ microcosms and stable isotope probing techniques. FEMS Microbiol Ecol 71: 237-246.
4. Chen Y, Murrell JC. (2010). When metagenomics meets stable-isotope probing: progress and perspectives. Trends Microbiol 18: 157-163.
5. Futamata H, Harayama S, Watanabe K. (2001). Groupspecific monitoring of phenol hydroxylase genes for a functional assessment of phenol-stimulated trichloroethylene bioremediation. Appl Environ Microbiol 67: 4671-4677.
6. Greenberg AE, Clesceri LS, Eaton AD. (2005). Standard methods for the examination of water and wastewater. American Public Health Association (APHA): Washington, DC, USA.
7. Handelsman J. (2004). Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 68: 669-685.
8. Huang WE, Griffiths RI, Thompson IP, Bailey MJ, Whiteley AS. (2004). Raman microscopic analysis of single microbial cells. Anal Chem 76: 4452-4458.
9. Huang WE, Stoecker K, Griffiths R, Newbold L, Daims H, Whiteley AS et al. (2007). Raman-FISH: combining stable-isotope Raman spectroscopy and fluorescence in situ hybridization for the single cell analysis of identity and function. Environ Microbiol 9: 1878-1889.
10. Huang WE, Ferguson A, Singer AC, Lawson K, Thompson IP, Kalin RM et al. (2009). Resolving genetic functions within microbial populations: in situ analyses using rRNA and mRNA stable isotope probing coupled with single-cell Raman-fluorescence in situ yybridization. Appl Environ Microbiol 75: 234-241.
11. Janssen PJ, Van Houdt R, Moors H, Monsieurs P, Morin N, Michaux A et al. (2010). The complete genome sequence of Cupriavidus metallidurans strain CH34, a master survivalist in harsh and anthropogenic environments. PLoS ONE 5: e10433.
12. Kaeberlein T, Lewis K, Epstein SS. (2002). Isolating ^quot;uncultivable^quot; microorganisms in pure culture in a simulated natural environment. Science 296: 1127-1129.
13. Kim JY, Kim JK, Lee SO, Kim CK, Lee K. (2005). Multicomponent phenol hydroxylase-catalysed formation of hydroxyindoles and dyestuffs from indole and its derivatives. Lett Appl Microbiol 41: 163-168.
14. Kubista M, Akerman B, Norden B. (1987). Characterization of interaction between DNA and 4',6-diamidino-2-phenylindole by optical spectroscopy. Biochemistry (Mosc) 26: 4545-4553.
15. Li MQ, Huang WE, Gibson CM, Fowler PW, Jousset A. (2013). Stable isotope probing and Raman apectroscopy for monitoring carbon flow in a food chain and revealingmetabolic pathway. Anal Chem 85: 1642-1649.
16. Manefield M, Whiteley AS, Griffiths RI, Bailey MJ. (2002). RNA stable isotope probing, a novel means of linking microbial community function to phylogeny. Appl Environ Microbiol 68: 5367-5373.
17. Marchesi JR, Sato T, Weightman AJ, Martin TA, Fry JC, Hiom SJ et al. (1998). Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA. Appl Environ Microbiol 64: 795-799.
18. McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A et al. (2012). An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J 6: 610-618.
19. Nelson CE, Carlson CA. (2012). Tracking differential incorporation of dissolved organic carbon types among diverse lineages of Sargasso Sea bacterioplankton. Environ Microbiol 14: 1500-1516.
20. Neufeld JD, Vohra J, Dumont MG, Lueders T, Manefield M, Friedrich MW et al. (2007). DNA stable-isotope probing. Nat Protoc 2: 860-866.
21. Pernthaler A, Dekas AE, Brown CT, Goffredi SK, Embaye T, Orphan VJ. (2008). Diverse syntrophic partnerships from-deep-sea methane vents revealed by direct cell capture and metagenomics. Proc Natl Acad Sci USA 105: 7052-7057.
22. Radajewski S, Ineson P, Parekh NR, Murrell JC. (2000). Stable-isotope probing as a tool in microbial ecology. Nature 403: 646-649.
23. Rappe MS, Giovannoni SJ. (2003). The uncultured microbial majority. Annu Rev Microbiol 57: 369-394.
24. Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng JF et al. (2013). Insights into the phylogeny and coding potential of microbial dark matter. Nature 499: 431-437.
25. Schleifer KH. (2004). Microbial diversity: Facts, problems and prospects. Syst Appl Microbiol 27: 3-9.
26. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB et al. (2009). Introducing mothur: opensource, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 7537-7541.
27. Sun JQ, Xu L, Tang YQ, Chen FM, Wu XL. (2012). Simultaneous degradation of phenol and n-hexadecane by Acinetobacter strains. Bioresour Technol 123: 664-668.
28. Vajrala N, Martens-Habbena W, Sayavedra-Soto LA, Schauer A, Bottomley PJ, Stahl DA et al. (2013). Hydroxylamine as an intermediate in ammonia oxidation by globally abundant marine archaea. Proc Natl Acad Sci USA 110: 1006-1011.
29. Vartoukian SR, Palmer RM, Wade WG. (2010). Strategies for culture of 'unculturable' bacteria. FEMS Microbiol Lett 309: 1-7.
30. Wang Y, Chen Y, Zhou Q, Huang S, Ning K, Xu J et al. (2012). A culture-independent approach to unravel uncultured bacteria and functional genes in a complex microbial community. PLoS ONE 7: e47530.
31. Wang Y, Ji YT, Wharfe ES, Meadows RS, March P, Goodacre R et al. (2013). Raman activated cell ejection for isolation of single cells. Anal Chem 85: 10697-10701.
32. Whitman WB, Coleman DC, Wiebe WJ. (1998). Prokaryotes: the unseen majority. Proc Natl Acad Sci USA 95: 6578-6583.
33. Zengler K, Toledo G, Rappe M, Elkins J, Mathur EJ, Short JM et al. (2002). Cultivating the uncultured. Proc Natl Acad Sci USA 99: 15681-15686.
34. Zhang D, Fakhrullin RF, Ozmen M, Wang H, Wang J, Paunov VN et al. (2011). Functionalization of wholecell bacterial reporters with magnetic nanoparticles. Microbial Biotech 4: 89-97.